Variant report

Variant	rs12500929
Chromosome Location	chr4:124623291-124623292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:124591127..124594016-chr4:124622193..124624753,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRY1-2	chr4:124623121-124623773	NONHSAT098194

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11726784	0.85[EUR][1000 genomes]
rs11735849	0.88[EUR][1000 genomes]
rs12054499	0.84[EUR][1000 genomes]
rs13113892	0.85[EUR][1000 genomes]
rs13117506	0.84[EUR][1000 genomes]
rs13117812	0.84[EUR][1000 genomes]
rs1364875	0.83[EUR][1000 genomes]
rs1425414	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2042627	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042628	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553356	0.84[EUR][1000 genomes]
rs2553366	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2553370	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2589838	0.87[EUR][1000 genomes]
rs2589845	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2589854	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2589855	0.83[EUR][1000 genomes]
rs2589856	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34182893	0.80[EUR][1000 genomes]
rs35748127	0.88[EUR][1000 genomes]
rs62319743	0.82[EUR][1000 genomes]
rs6837781	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6838030	0.81[AMR][1000 genomes]
rs72670521	0.81[ASN][1000 genomes]
rs72670522	0.81[ASN][1000 genomes]
rs72670525	0.81[ASN][1000 genomes]
rs72670526	0.81[ASN][1000 genomes]
rs7657498	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890181	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890182	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs890183	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9307531	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv469710	chr4:124474286-124623722	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv482747	chr4:124474286-124623722	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830047	chr4:124504051-124699142	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12500929	ADAD1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124618400-124632000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:124621600-124627800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:124621600-124631400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:124622000-124630600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:124622000-124636200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:124622000-124637200	Weak transcription	Psoas Muscle	Psoas
7	chr4:124622200-124623400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:124622200-124624200	Weak transcription	Aorta	Aorta
9	chr4:124622400-124623400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:124622400-124623400	Enhancers	NHDF-Ad	bronchial
11	chr4:124622800-124623400	Enhancers	NHLF	lung
12	chr4:124622800-124627800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:124623000-124623400	Enhancers	Fetal Muscle Leg	muscle
14	chr4:124623200-124624000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:124623200-124628200	Weak transcription	Osteobl	bone

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